On 11/23/2011 01:18 PM, James Starlight wrote: > Thanks Thomas! > > Those scripts works fine. Could you tell me if there any way to install > all of those scripts as the pymol plugins ( that I need not to load this > scripts every time when I sttart pymol de novo )? > > > James >
Hi James Jason Vertrees has previously responded to a similar question: http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg09579.html This is the essence of the email: Put the following code (after editing the /path/to/dir, obviously) in your .pymolrc -------------------------------------------------- python # make a list of all your directories w/scripts known_directories = [ "/path/to/dir1", "/path/to/dir2", ... ] import glob for p in known_directories: for f in glob.glob(p+/*.py"): cmd.do("run " + f) python end --------------------------------------------------- (see here http://www.pymolwiki.org/index.php/Launching_PyMOL for an explanation of the .pymolrc file) Hope this helps Best regards, Folmer > 2011/11/23 James Starlight <jmsstarli...@gmail.com > <mailto:jmsstarli...@gmail.com>> > > Thanks thomas > > Those scripts works fine. Could you tell me if there any way to > install all of those scripts as the pymol plugins ( that I need not > to load this scripts every time when I sttart pymol de novo )? > > > James > > > 2011/11/23 Thomas Holder <spel...@users.sourceforge.net > <mailto:spel...@users.sourceforge.net>> > > Hi James, > > check this PyMOLWiki page: http://pymolwiki.org/index.__php/Fab > <http://pymolwiki.org/index.php/Fab> > > However, the "fab" command does not take user defined phi/psi > angles, only 4 predefined conformations ("ss" argument). User > defined phi/psi can be handled by these scripts: > > http://pymolwiki.org/index.__php/CreateSecondaryStructure > <http://pymolwiki.org/index.php/CreateSecondaryStructure> > http://pldserver1.biochem.__queensu.ca/~rlc/work/pymol/#__model > <http://pldserver1.biochem.queensu.ca/%7Erlc/work/pymol/#model> > > Cheers, > Thomas > > James Starlight wrote, On 11/23/11 11:43: > > Dear PyMol Users! > > I wounder to know about possible ways of creation of the > peptide structures via PyMol Builder module. In particular I > need create a linear structure of my protein ( with fixed > phi and psi angles) for futher folding molecular dynamics > simulation of that peptide. But in builder module I found > only helix and sheet conformations for each aa. residue. How > I can specify desired values for both torsion angles ? > > Also I'd like to know is there any module for pymol wich > could be used for obtaining linear unfolded structure for > the defined sequence or folded protein ( in pdb) ? > > Thanks, > > > James > > > -- > Thomas Holder > MPI for Developmental Biology > Spemannstr. 35 > D-72076 Tübingen > > > > > > ------------------------------------------------------------------------------ > All the data continuously generated in your IT infrastructure > contains a definitive record of customers, application performance, > security threats, fraudulent activity, and more. Splunk takes this > data and makes sense of it. IT sense. And common sense. > http://p.sf.net/sfu/splunk-novd2d > > > > _______________________________________________ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net ------------------------------------------------------------------------------ All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-novd2d _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
